OLIGOMER user manual

Fitting the experimental scattering curve from multicompoment mixture as a linear combination of the contribution of each component.

The program oligomer fits an experimental scattering curve from multicompoment mixture of proteins to find the volume fractions of each component in the mixture.

The input data for oligomer is experimental scattering curve from a mixture of several dictinct components and a set of form-factors for each component of this mixture.

The experimental scattering intensity I(s) from a mixture of K different particles (components) is written as:

I(s) = ∑(w_i×I_i(s))

where w_i and I_i(s) are the volume fraction and the scattering intensity from the i-th component, respectively.

Given the intensities from the components (form–factors), program oligomer finds the volume fractions by solving a system of linear equations using the algorithm of nonnegative or unconstrained least-squares to minimize the discrepancy between the experimental and calculated scattering curves.

X-ray or neutron form-factors of proteins with known structure or of dummy atoms models can be computed using the programs CRYSOL/CRYSON, which are parts of the ATSAS release.

Scattering intensity from the form-factors must be prepared in the columnar format:

1^st line: comment

from 2^nd line: scattering vector (s), iForm1, iForm2 ...

here, s = 4*π*sin (θ)/λ, [1/Angstroms)

Iform1, Iform2 etc are the scattering intensities of the components. They should be normalized in such a way that iForm(s=0) is equal (or proportional to) the square of the molecular weight MW (or total scattering length).

This program estimates molecular weights for calculation of volume fractions and radii of gyration from experimental or model scattering curves of components of the mixture. The latter values are used only for determination of the average value of radius of giration for all mixtures.

Therefore, you must enter the real values of MW for each component (for example, based on information about primary sequence) in following cases:

• scattering curves from components (i.e. sets of form-factors) are standartized to I_exp(0) = 1
• scattering curves from components calculated by CRYDAM or CRYSOL from dummy atom models built by programs DAMMIN or GASBOR with beads not equal size
• sets of form-factors are standartized to equally values of I_exp(0)

If the iForm curves and not properly scaled, the fit not be affected but the volume fractions will be incorrect.

If one just uses predicted CRYSOL curves from different oligomers, no additional normalization of the form factors is required.

After starting oligomer you will need to specify:

1. Form-factor file
2. Experimental data file and for data in OTOKO format file contained values of angular axis
3. Scale factor for angular units on Experimental File:
   "1" - units is Angstroms
   "2" - units is nm
   If entered value will be more then 2 and less then 1, then default value is equal to 1.
4. Fraction of experimental data which will processed.
   If entered value will be more then 1 and less then 0, then default value is equal to 1.
5. Name of Output file (default value: "oligomer.log")

After the program is finished, you will get the files:

oligomer can also be used in batch mode with "/" batch options.

Use in the batch mode:

oligomer [ /ff ]  [ ]  [ /param1 ] ... [ /paramN ]

where the arguments FF_File and Dat_File (experimental scattering data file name) should be the name of a ASCII format file (extension .dat or .txt).

Wildcards (e.g. m?.dat or *.dat) are permitted, in which case the program makes a loop over these files.
If Dat_File is not specified or Dat_File = all then all DAT files will be processed.
The command option "/dat" is optional for Dat_File and can be omitted.

The following program options can be given as keys with parameters:

Examples:

oligomer  /ff  ff.dat  /dat  m01.dat  /un  2
for fitting m01.dat file using the formfactor file ff.dat with the angular axis in nm^-1

oligomer  /ff  ff2.dat  m*.dat  /smin 0.5  /pl  /br
for processing all experimental data files with the names beginning with "m" and with "dat" extension using the formfactor file ff2.dat. The fitting will be applied from smin=0.5 for the experimental curves.
The fits will be plotted and output oligomer.log file will have the brief format.

oligomer  /ff  ff3.dat  m03.dat  /out  m03.log  /un  3
for fitting m03.dat file using the formfactor file ff3.dat with the angular units 3 (2π*s, Å^-1).

Back to oligomer page.